It is often desirable to determine the abundance or relative concentration of particular nucleic acid sequences. Such nucleic acid sequences include, for example, chromosomes, genome sequences, mRNAs, peptides, genotypes, or haplotypes. Various tools for mapping or aligning nucleic acid sequences to a reference sequence are known and used. However the available techniques are often not tailored for the needs of a particular application such as determining chromosomal abundance. For example, the available techniques often provide both relevant and irrelevant information for the application at hand. As a consequence, they may not be optimized for rapidly providing the relevant information.